Cell-based clustering using pixel clusters: Gaussian blur sigma=2, pixel clusters hClusters using z-score cap=0,3 and iter thresh=3, normalize by total, k=30

1 Heatmaps of pixel clusters x markers

2 Compare pixel clusering with cell clustering

3 Cell-based FlowSOM clustering using pixel hierarchical clusters

3.1 All hClusts

3.1.1 Cell cluster x frequency of pixel clusters

3.1.2 Cell cluster x marker

3.2 Drop hClusts using z-score of # of clusters

## [1] "# clusters in each hClust"

## 
##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 
## 49  4  2  3  3  3  2  2  2  6  1  1  4  3  1  5  2  3  3  1

## [1] "Z-score of # clusters in each hClust"

##  [1]  4.21341854 -0.09575951 -0.28727854 -0.19151902 -0.19151902 -0.19151902
##  [7] -0.28727854 -0.28727854 -0.28727854  0.09575951 -0.38303805 -0.38303805
## [13] -0.09575951 -0.19151902 -0.38303805  0.00000000 -0.28727854 -0.19151902
## [19] -0.19151902 -0.38303805

## [1] "Number of hClusts to drop: 1"

## [1] "hClusts to drop: 1"

## [1] "# cells discarded because sum of freq=0: 11115"

3.2.1 Cell cluster x frequency of pixel clusters

3.2.2 Cell cluster x marker

3.3 Drop hClusts using rank of marker expression (must be in top 2)

## [1] "Number of hClusts to drop: 2"

## [1] "hClusts to drop: 1,4"

## [1] "# cells discarded because sum of freq=0: 13075"

3.3.1 Cell cluster x frequency of pixel clusters

3.3.2 Cell cluster x marker

3.4 Iterative hClusts

3.4.1 Cell cluster x frequency of pixel clusters

3.4.2 Cell cluster x marker

3.5 Iterative hClusts, drop hClusts using rank of marker expression (must be in top 2)

## [1] "Number of iter_hClusts to drop: 19"

## [1] "iter_hClusts to drop: 37,38,22,39,40,41,24,42,43,4,44,27,28,30,31,33,34,35,36"

## [1] "# cells discarded because sum of freq=0: 7120"

3.5.1 Cell cluster x frequency of pixel clusters

3.5.2 Cell cluster x marker

4 Cell-based FlowSOM clustering using pixel clusters

4.1 All clusters

4.1.1 Cell cluster x frequency of pixel clusters

4.1.2 Cell cluster x marker

4.2 Drop clusters using rank of marker expression (must be in top 6)

## [1] "Number of clusters to drop: 36"

## [1] "Clusters to drop: 60,57,56,45,46,47,48,35,55,43,66,67,59,53,26,24,64,69,77,76,75,86,27,14,95,44,34,78,84,54,73,65,58,96,52,25"

## [1] "# cells discarded because sum of freq=0: 7235"

4.2.1 Cell cluster x frequency of pixel clusters

4.2.2 Cell cluster x marker